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- PDB-4qdc: Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) ... -

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Basic information

Entry
Database: PDB / ID: 4qdc
TitleCrystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with FE2/S2 (INORGANIC) CLUSTER
Components3-ketosteroid 9alpha-hydroxylase oxygenase
KeywordsOXIDOREDUCTASE / Mixed Function Oxygenases
Function / homology
Function and homology information


3-ketosteroid 9alpha-monooxygenase / 3-ketosteroid 9-alpha-monooxygenase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
3-ketosteroid-9-alpha-monooxygenase, oxygenase component-like, C-terminal domain / 3-Ketosteroid 9alpha-hydroxylase C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. ...3-ketosteroid-9-alpha-monooxygenase, oxygenase component-like, C-terminal domain / 3-Ketosteroid 9alpha-hydroxylase C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-ANDROSTENE-3-17-DIONE / : / FE2/S2 (INORGANIC) CLUSTER / 3-ketosteroid-9-alpha-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPenfield, J. / Worrall, L.J. / Strynadka, N.C. / Eltis, L.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Substrate specificities and conformational flexibility of 3-ketosteroid 9 alpha-hydroxylases.
Authors: Penfield, J.S. / Worrall, L.J. / Strynadka, N.C. / Eltis, L.D.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1987
Polymers44,2971
Non-polymers9006
Water4,972276
1
A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules

A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules

A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,59321
Polymers132,8913
Non-polymers2,70118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13360 Å2
ΔGint-146 kcal/mol
Surface area44230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.183, 162.183, 46.969
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-ketosteroid 9alpha-hydroxylase oxygenase


Mass: 44297.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: ksha, kshA5 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 / References: UniProt: F1CMY8

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Non-polymers , 7 types, 282 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


Mass: 286.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.8 M NaH2PO4, 0.2 M K2HPO4, 2% PEG-3000, 20 mM CHES, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.92 Å
DetectorType: Rayonix MX300HE CCD X-ray detector / Detector: CCD / Date: Feb 24, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→44.54 Å / Num. obs: 49275 / % possible obs: 88.1 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 18
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.9-1.947.9212848162045.9
9.11-44.548.672.3483856499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASERphasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
MxDCdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zyl

2zyl


Resolution: 1.9→140.45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.1767 / WRfactor Rwork: 0.1501 / FOM work R set: 0.812 / SU B: 3.122 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1189 / SU Rfree: 0.1169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2459 5 %RANDOM
Rwork0.1866 ---
obs0.1882 49074 87.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 116.45 Å2 / Biso mean: 30.161 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→140.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 50 276 3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193121
X-RAY DIFFRACTIONr_bond_other_d0.0010.022825
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9414243
X-RAY DIFFRACTIONr_angle_other_deg0.81636505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08824.085164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7781521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_mcbond_it4.172.6871477
X-RAY DIFFRACTIONr_mcbond_other4.1622.6831476
X-RAY DIFFRACTIONr_mcangle_it5.3294.0091845
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.544 100 -
Rwork0.514 1695 -
all-1795 -
obs--43.44 %

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